China has indicted the outspoken Uighur scholar Ilham Tohti on charges of separatism, prosecutors have announced.

Tohti, who has been detained since January, was not informed of the latest move directly, according to his lawyer, who accused authorities of "shocking" handling of the case and ignoring Tohti's rights to a defence.

Supporters of the economics professor say he has not advocated independence for the north-western region of Xinjiang and that the case against him is retaliation for criticising government policies and questioning official accounts of violence in or related to the region.

Before he was seized at his home in Beijing, Tohti was a rare voice for Uighur dissatisfaction within China. Beijing says it respects local identity and has invested heavily in the region to boost living standards, but many in the Muslim Uighur community are unhappy at cultural and religious restrictions, Han migration and development that they believe has benefited others more than them. Han Chinese make up almost 92% of the country's population.

Prosecutors in Xinjiang's capital, Urumqi, where Tohti is held, announced his indictment in a statement posted online. Once charged, conviction is all but certain, particularly in such a high-profile case. Separatism charges in theory carry the death penalty, though they usually result in imprisonment.

Tohti's daughter Jewher Ilham, who is studying in the US, said: "I am angry about this, they have not followed the legal path. My father was only trying to foster a dialogue. What they have charged him with is untrue."

Tohti's lawyer Li Fangping, who was not allowed to see his client until June, said: "I just saw online that Ilham Tohti's case has been transferred to the court and it is quite shocking. Urumqi's procuratorate has not replied to our verbal or written requests, which are both legitimate and justifiable, for copies of audio-visual material.

"The procuratorate has failed to follow the proper procedure of informing the defence lawyer of their decision to formally charge Ilham Tohti with separatism. I am very shocked by the procuratorate's lack of respect for the right to a defence."

Shortly after Tohti's detention, police alleged that he had used the website he founded to recruit and manipulate people to "make rumours, distort and hype up issues in a bid to create conflicts, spread separatist thinking, incite ethnic hatred, advocate 'Xinjiang independence' and conduct separatist activities."

They also alleged that in classes he had said Uighurs should engage in violent struggle, and encouraged students to hate China, subvert the government and emulate Chinese who resisted Japanese invaders in the second world war in their opposition to the government.

Several of his students were also detained in January. It is not clear whether all of them have been released.

Sophie Richardson, China director at Human Rights Watch, said: "When someone as constructive and as dedicated to finding common ground between ethnic minorities is charged with separatism, it is extremely difficult to find room for optimism about Xi Jinping's ethnic minority policies. It's no longer clear to me what Beijing wants other than the apparent eradication of any criticism – no matter how mild, peaceful or constructive; no matter whether it's wholly within the confines of Chinese law."

The PEN American Centre, which gave Tohti an award this year, said in a statement: "Tohti … has never advocated violence or the separation of Xinjiang from China. Instead, he has worked within the country's laws to promote equal rights for all of China's citizens, and to encourage exchange and understanding between different ethnic groups.

"The charges against Ilham Tohti reflect the Chinese government's refusal to distinguish between peaceful advocacy and violent unrest. By targeting Tohti based on his ideas, writings, and teachings, Beijing sends the message that advocacy for Uighur rights is prohibited in any form. The government claims an aim to discourage violence, but the denial of peaceful means of expression risks having the exact opposite effect."